We have implemented a control system core for experiments in atomic, molecular, and optical physics based on a commercial low-cost board, featuring a field-programmable gate array as part of a system-on-a-chip on which a Linux operating system is running. The board features Gigabit Ethernet, allowing for fast data transmission and operation of remote experimental systems. A single board can control a set of devices generating digital, analog, and radio frequency signals with precise timing given either by an external or internal clock. Contiguous output and input sampling rates of up to 40 MHz are achievable. Several boards can run synchronously with a timing error approaching 1 ns. For this purpose, a novel auto-synchronization scheme is demonstrated, with possible application in complex distributed experimental setups with demanding timing requests.